Epidemiological feedbacks affect evolutionary emergence of pathogens

American Naturalist

Volumn 183, Issue 4, 2014, Pages

  Hartfield, Matthew ^a   Alizon, Samuel ^a  

^a INSTITUT DE RECHERCHE POUR LE DÉVELOPPEMENT   (France)

Author keywords

Changing population sizes; Chikungunya virus; Epidemiology; Evolution; Outbreaks; Pathogen emergence

Indexed keywords

ADAPTATION; DISEASE INCIDENCE; EPIDEMIOLOGY; FECUNDITY; MUTATION; PATHOGEN; POPULATION DYNAMICS; VIRUS;

MASCARENE ISLANDS; REUNION;

BIOLOGICAL MODEL; CHIKUNGUNYA FEVER; COMMUNICABLE DISEASE; COMPUTER SIMULATION; DISEASE TRANSMISSION; EPIDEMIC; EVOLUTION; GENETICS; HOST PATHOGEN INTERACTION; HUMAN; INDIAN OCEAN; MUTATION;

BIOLOGICAL EVOLUTION; CHIKUNGUNYA FEVER; COMMUNICABLE DISEASES, EMERGING; COMPUTER SIMULATION; DISEASE OUTBREAKS; DISEASE TRANSMISSION, INFECTIOUS; HOST-PATHOGEN INTERACTIONS; HUMANS; INDIAN OCEAN ISLANDS; MODELS, GENETIC; MUTATION;

EID: 84896459717     PISSN: 00030147     EISSN: None     Source Type: Journal    
DOI: 10.1086/674795     Document Type: Article

References (64)

1. Abramowitz, M., and I. Stegun. 1970. Handbook of mathematical functions. Dover, New York.
2. Akahata, W., Z.-Y. Yang, H. Andersen, S. Sun, H. A. Holdaway, W.-P. Kong, M. G. Lewis, et al. 2010. A virus-like particle vaccine for epidemic Chikungunya virus protects nonhuman primates against infection. Nature Medicine 16:334-338.
3. Alexander, H. K., and S. Bonhoeffer. 2012. Pre-existence and emergence of drug resistance in a generalized model of intra-host viral dynamics. Epidemics 4:187-202.
4. Alexander, H. K., and T. Day. 2010. Risk factors for the evolutionary emergence of pathogens. Journal of the Royal Society Interface 7: 1455-1474.
5. Allen, L. 2008. An introduction to stochastic epidemic models. Pages 81-130 in F. Brauer, P. van den Driessche, and J. Wu, eds. Mathematical epidemiology. Lecture Notes in Mathematics. Vol. 1945. Springer, Berlin.
6. Allen, L. J. S., and A. M. Burgin. 2000. Comparison of deterministic and stochastic SIS and SIR models in discrete time. Mathematical Biosciences 163:1-33.
7. Anderson, R. M., and R. M. May. 1991. Infectious diseases of humans: dynamics and control. Oxford University Press, Oxford.
8. André, J.-B., and T. Day. 2005. The effect of disease life history on the evolutionary emergence of novel pathogens. Proceedings of the Royal Society B: Biological Sciences 272:1949-1956.
9. André, J.-B., and M. E. Hochberg. 2005. Virulence evolution in emerging infectious diseases. Evolution 59:1406-1412.
10. Antia, R., R. R. Regoes, J. C. Koella, and C. T. Bergstrom. 2003. The role of evolution in the emergence of infectious diseases. Nature 426:658-661.
11. Arinaminpathy, N., and A. R. McLean. 2009. Evolution and emergence of novel human infections. Proceedings of the Royal Society B: Biological Sciences 276:3937-3943.
12. Barton, N. H. 1994. The reduction in fixation probability caused by substitutions at linked loci. Genetics Research 64:199-208.
13. Barton, N. H. 2000. Genetic hitchhiking. Philosophical Transactions of the Royal Society B: Biological Sciences 355:1553-1562.
14. Benmayor, R., D. J. Hodgson, G. G. Perron, and A. Buckling. 2009. Host mixing and disease emergence. Current Biology 19:764-767.
15. Cherian, S. S., A. M. Walimbe, S. M. Jadhav, S. S. Gandhe, S. L. Hundekar, A. C. Mishra, and V. A. Arankalle. 2009. Evolutionary rates and timescale comparison of Chikungunya viruses inferred from the whole genome/E1 gene with special reference to the 2005-07 outbreak in the Indian subcontinent. Infection, Genetics and Evolution 9:16-23.
16. de Lamballerie, X., E. Leroy, R. Charrel, K. Ttsetsarkin, S. Higgs, and E. Gould. 2008. Chikungunya virus adapts to tiger mosquito via evolutionary convergence: a sign of things to come? Virology Journal 5:33.
17. Dennehy, J. J. 2009. Bacteriophages as model organisms for virus emergence research. Trends in Microbiology 17:450-457.
18. Diekmann, O., and J. Heesterbeek. 2000. Mathematical epidemiology of infectious diseases: model building, analysis and interpretation. Wiley, Chichester.
19. Eyre-Walker, A., and P. D. Keightley. 2007. The distribution of fitness effects of new mutations. Nature Reviews Genetics 8:610-618.
20. Fargette, D., G. Konaté, C. Fauquet, E. Muller, M. Peterschmitt, and J. M. Thresh. 2006. Molecular ecology and emergence of tropical plant viruses. Annual Review of Phytopathology 44:235-260.
21. Ferguson, N. M., A. P. Galvani, and R. M. Bush. 2003. Ecological and immunological determinants of influenza evolution. Nature 422:428-433.
22. Frost, W. H. 1919. The epidemiology of influenza. Public Health Reports (1896-1970) 34:1823-1836.
23. Galvani, A. P., and R. M. May. 2005. Epidemiology: dimensions of superspreading. Nature 438:293-295.
24. Gandon, S., and T. Day. 2008. Evidences of parasite evolution after vaccination. Vaccine 26(suppl. 3):C4-C7.
25. Gandon, S., M. E. Hochberg, R. D. Holt, and T. Day. 2013. What limits the evolutionary emergence of pathogens? Philosophical Transactions of the Royal Society B: Biological Sciences 368: 20120086.
26. Gillespie, D. T. 1977. Exact stochastic simulation of coupled chemical reactions. Journal of Physical Chemistry 81:2340-2361.
27. Gillespie, D. T. 2001. Approximate accelerated stochastic simulation of chemically reacting systems. Journal of Physical Chemistry 115: 1716-1733.
28. Gonzalez, A., O. Ronce, R. Ferriere, and M. E. Hochberg. 2013. Evolutionary rescue: an emerging focus at the intersection between ecology and evolution. Philosophical Transactions of the Royal Society B: Biological Sciences 368:20120404.
29. Hansen, E., and T. Day. 2011. Optimal antiviral treatment strategies and the effects of resistance. Proceedings of the Royal Society B: Biological Sciences 278:1082-1089.
30. Hartfield, M., and S. Alizon. 2013a. Data from: Epidemiological feedbacks affect evolutionary emergence of pathogens. Amercan Naturalist, Dryad Digital Repository, http://dx.doi.org/10.5061 /dryad.kj238.
31. Hartfield, M., and S. Alizon. 2013b. Introducing the outbreak threshold in epidemiology. PLoS Pathogens 9:e1003277.
32. Hartfield, M., and S. P. Otto. 2011. Recombination and hitchhiking of deleterious alleles. Evolution 65:2421-2434.
33. Iwasa, Y., F. Michor, and M. A. Nowak. 2003. Evolutionary dynamics of escape from biomedical intervention. Proceedings of the Royal Society B: Biological Sciences 270:2573-2578.
34. Iwasa, Y., F. Michor, and M. A. Nowak. 2004. Evolutionary dynamics of invasion and escape. Journal of Theoretical Biology 226:205-214.
35. Karlin, S., and H. M. Taylor. 1981. A second course in stochastic processes. Academic Press, New York.
36. Keeling, M. J., and P. Rohani. 2007. Modeling infectious diseases in humans and animals. Princeton University Press, Princeton, NJ.
37. Kimura, M. 1983. The neutral theory of molecular evolution. Cambridge University Press, Cambridge.
38. Kubiak, R. J., N. Arinaminpathy, and A. R. McLean. 2010. Insights into the evolution and emergence of a novel infectious disease. PLoS Computational Biology 6:e1000947.
39. Little, T. J., and A. R. Kraaijeveld. 2004. Ecological and evolutionary implications of immunological priming in invertebrates. Trends in Ecology and Evolution 19:58-60.
40. Little, T. J., B. O'Connor, N. Colegrave, K. Watt, and A. F. Read. 2003. Maternal transfer of strain-specific immunity in an invertebrate. Current Biology 13:489-492.
41. Lloyd-Smith, J. O., P. C. Cross, C. J. Briggs, M. Daugherty, W. M. Getz, J. Latto, M. S. Sanchez, A. B. Smith, and A. Swei. 2005a. Should we expect population thresholds for wildlife disease? Trends in Ecology and Evolution 20:511-519.
42. Lloyd-Smith, J. O., S. J. Schreiber, P. E. Kopp, andW. M. Getz. 2005b. Superspreading and the effect of individual variation on disease emergence. Nature 438:355-359.
43. Lourenco, J., and M. Recker. 2010. Viral and epidemiological determinants of the invasion dynamics of novel dengue genotypes. PLoS Neglected Tropical Diseases 4:e894.
44. Martin, G., R. Aguilée, J. Ramsayer, O. Kaltz, and O. Ronce. 2013. The probability of evolutionary rescue: towards a quantitative comparison between theory and evolution experiments. Philosophical Transactions of the Royal Society B: Biological Sciences 368:20120088.
45. Maynard Smith, J., and J. Haigh. 1974. The hitch-hiking effect of a favourable gene. Genetics Research 23:23-35.
46. McCallum, H., N. Barlow, and J. Hone. 2001. How should pathogen transmission be modelled? Trends in Ecology and Evolution 16: 295-300.
47. Méthot, P.-O., and S. Alizon. 2014. Emerging diseases and the evolution of virulence: the case of the Spanish influenza pandemic. In G. Lambert, P. Huneman, and M. Silberstein, eds. Disease, classification, and evidence. New Essays in the Philosophy of Medicine. Springer (forthcoming).
48. Moreira, L. A., I. Iturbe-Ormaetxe, J. A. Jeffery, G. Lu, A. T. Pyke, L. M. Hedges, B. C. Rocha, et al. 2009. A Wolbachia symbiont in Aedes aegypti limits infection with dengue, chikungunya, and Plasmodium. Cell 139:1268-1278.
49. Otto, S. P., and N. H. Barton. 1997. The evolution of recombination: removing the limits to natural selection. Genetics 147:879-906.
50. Otto, S. P., and M. C. Whitlock. 1997. The probability of fixation in populations of changing size. Genetics 146:723-733.
51. Pérez-Reche, F. J., F. M. Neri, S. N. Taraskin, and C. A. Gilligan. 2012. Prediction of invasion from the early stage of an epidemic. Journal of the Royal Society Interface 9:2085-2096.
52. Renault, P., J.-L. Solet, D. Sissoko, E. Balleydier, S. Larrieu, L. Filleul, C. Lassalle, et al. 2007. A major epidemic of Chikungunya virus infection on Réunion Island, France, 2005-2006. American Journal of Tropical Medicine and Hygiene 77:727-731.
53. Sadd, B. M., Y. Kleinlogel, R. Schmid-Hempel, and P. Schmid-Hempel. 2005. Trans-generational immune priming in a social insect. Biology Letters 1:386-388.
54. Sadd, B. M., and P. Schmid-Hempel. 2007. Facultative but persistent trans-generational immunity via the mother's eggs in bumblebees. Current Biology 17:R1046-R1047.
55. Schuffenecker, I., I. Iteman, A. Michault, S. Murri, L. Frangeul, M.-C. Vaney, R. Lavenir, et al. 2006. Genome microevolution of Chikungunya viruses causing the Indian Ocean outbreak. PLoS Medicine 3:e263 EP.
56. Sniegowski, P. D., P. J. Gerrish, T. Johnson, and A. Shaver. 2000. The evolution of mutation rates: separating causes from consequences. BioEssays 22:1057-1066.
57. Vazeille, M., S. Moutailler, D. Coudrier, C. Rousseaux, H. Khun, M. Huerre, J. Thiria, et al. 2007. Two Chikungunya isolates from the outbreak of La Reunion (Indian Ocean) exhibit different patterns of infection in the mosquito, Aedes albopictus. PLoS ONE 2:e1168.
58. Volk, S. M., R. Chen, K. A. Tsetsarkin, A. P. Adams, T. I. Garcia, A. A. Sall, F. Nasar, et al. 2010. Genome-scale phylogenetic analyses of Chikungunya virus reveal independent emergences of recent epidemics and various evolutionary rates. Journal of Virology 84: 6497-6504.
59. Wang, D., A. Suhrbier, A. Penn-Nicholson, J. Woraratanadharm, J. Gardner, M. Luo, T. T. Le, et al. 2011. A complex adenovirus vaccine against Chikungunya virus provides complete protection against viraemia and arthritis. Vaccine 29:2803-2809.
60. Wauquier, N., P. Becquart, D. Nkoghe, C. Padilla, A. Ndjoyi-Mbiguino, and E. M. Leroy. 2011. The acute phase of Chikungunya virus infection in humans is associated with strong innate immunity and T CD8 cell activation. Journal of Infectious Diseases 204:115-123.
61. Wolfe, N. D., C. P. Dunavan, and J. Diamond. 2007. Origins of major human infectious diseases. Nature 447:279-283.
62. Woolhouse, M., F. Scott, Z. Hudson, R. Howey, and M. Chase-Topping. 2012. Human viruses: discovery and emergence. Philosophical Transactions of the Royal Society B: Biological Sciences 367: 2864-2871.
63. Woolhouse, M. E. J., C. Dye, J.-F. Etard, T. Smith, J. D. Charlwood, G. P. Garnett, P. Hagan, et al. 1997. Heterogeneities in the transmission of infectious agents: implications for the design of control programs. Proceedings of the National Academy of Sciences of the USA 94:338-342.
64. Yates, A., R. Antia, and R. R. Regoes. 2006. How do pathogen evolution and host heterogeneity interact in disease emergence? Proceedings of the Royal Society B: Biological Sciences 273:3075-3083.